Class N. 2 Assignment

Part 1: Benchling & In-silico Gel Art

See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details. Overview:

[x] Make a free account at benchling.com
[x] Import the Lambda DNA.
[x] Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI
[x] Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks.

arbol solo.png

Part 2: Gel Art - Restriction Digests and Gel Electrophoresis

Optional for Committed Listeners with Lab Access. Mandatory for MIT/Harvard Students. Documentation due start of class Feb 18

Perform the lab experiment you designed in Part 1 and outlined in the Gel Art: Restriction Digests and Gel Electrophoresis protocol.

Still working to perform Gel Art!

Part 3: DNA Design Challenge

3.1. Choose your protein.

In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose.

[Example from our group homework, you may notice the particular format~~~ The example below came from UniProt]

sp|P03609|LYS_BPMS2 Lysis protein OS=Escherichia phage MS2 OX=12022 PE=2 SV=1 METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLL EAVIRTVTTLQQLLT

ismA The intestinal sterol metabolism A (ismA) gene in microbes encodes a set of cholesterol dehydrogenase enzymes that transform circulating cholesterol into coprostanol, a non-absorbable form of cholesterol that is eventually excreted in feces. This process plays a crucial role in regulating cholesterol levels within the body.